Multiple sequence alignment - TraesCS3B01G120000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G120000 chr3B 100.000 4977 0 0 1 4977 90111950 90116926 0.000000e+00 9191.0
1 TraesCS3B01G120000 chr3B 84.633 1321 156 27 2362 3653 89609694 89610996 0.000000e+00 1271.0
2 TraesCS3B01G120000 chr3B 91.575 546 39 2 890 1432 89583902 89584443 0.000000e+00 747.0
3 TraesCS3B01G120000 chr3B 85.350 314 42 3 3110 3422 89626407 89626717 6.220000e-84 322.0
4 TraesCS3B01G120000 chr3B 84.444 315 40 6 3770 4081 89627092 89627400 8.100000e-78 302.0
5 TraesCS3B01G120000 chr3B 84.566 311 37 8 3775 4081 89611052 89611355 1.050000e-76 298.0
6 TraesCS3B01G120000 chr3B 91.981 212 17 0 3442 3653 89626828 89627039 1.050000e-76 298.0
7 TraesCS3B01G120000 chr3B 89.316 234 25 0 1894 2127 89585404 89585637 1.350000e-75 294.0
8 TraesCS3B01G120000 chr3B 90.052 191 19 0 2169 2359 89585731 89585921 1.070000e-61 248.0
9 TraesCS3B01G120000 chr3B 96.364 55 1 1 3704 3757 758725720 758725774 6.860000e-14 89.8
10 TraesCS3B01G120000 chr3B 93.750 48 3 0 1483 1530 89584632 89584679 6.910000e-09 73.1
11 TraesCS3B01G120000 chr3B 100.000 28 0 0 703 730 147652233 147652260 9.000000e-03 52.8
12 TraesCS3B01G120000 chr3A 91.824 3180 178 34 1786 4941 66223462 66226583 0.000000e+00 4357.0
13 TraesCS3B01G120000 chr3A 87.393 1396 89 37 447 1786 66221366 66222730 0.000000e+00 1522.0
14 TraesCS3B01G120000 chr3A 88.730 976 102 5 1895 2869 66218271 66219239 0.000000e+00 1186.0
15 TraesCS3B01G120000 chr3A 92.105 532 38 1 901 1432 66216375 66216902 0.000000e+00 747.0
16 TraesCS3B01G120000 chr3A 81.881 872 121 20 2849 3696 66219283 66220141 0.000000e+00 701.0
17 TraesCS3B01G120000 chr3A 83.544 474 63 10 3746 4213 66220122 66220586 3.560000e-116 429.0
18 TraesCS3B01G120000 chr3A 91.667 48 4 0 1483 1530 66217167 66217214 3.220000e-07 67.6
19 TraesCS3B01G120000 chr3D 93.712 1638 92 6 1786 3419 57153384 57155014 0.000000e+00 2444.0
20 TraesCS3B01G120000 chr3D 94.360 1117 36 12 3419 4531 57158266 57159359 0.000000e+00 1688.0
21 TraesCS3B01G120000 chr3D 87.991 1374 95 22 387 1706 57151208 57152565 0.000000e+00 1559.0
22 TraesCS3B01G120000 chr3D 87.523 1090 114 14 1907 2983 56848697 56847617 0.000000e+00 1240.0
23 TraesCS3B01G120000 chr3D 90.842 546 43 2 890 1432 56850673 56850132 0.000000e+00 725.0
24 TraesCS3B01G120000 chr3D 86.694 496 63 2 3158 3653 56847410 56846918 9.420000e-152 547.0
25 TraesCS3B01G120000 chr3D 91.076 381 26 3 4549 4922 57159739 57160118 4.450000e-140 508.0
26 TraesCS3B01G120000 chr3D 83.186 452 65 7 3769 4217 56846891 56846448 2.160000e-108 403.0
27 TraesCS3B01G120000 chr3D 85.393 89 11 2 110 197 57150924 57151011 1.910000e-14 91.6
28 TraesCS3B01G120000 chr3D 97.500 40 0 1 4866 4905 57160113 57160151 3.220000e-07 67.6
29 TraesCS3B01G120000 chr4A 84.633 1321 156 27 2362 3653 609324307 609325609 0.000000e+00 1271.0
30 TraesCS3B01G120000 chr4A 85.350 314 42 3 3110 3422 609343581 609343891 6.220000e-84 322.0
31 TraesCS3B01G120000 chr4A 84.444 315 40 6 3770 4081 609344266 609344574 8.100000e-78 302.0
32 TraesCS3B01G120000 chr4A 84.566 311 37 8 3775 4081 609325665 609325968 1.050000e-76 298.0
33 TraesCS3B01G120000 chr4A 91.981 212 17 0 3442 3653 609344002 609344213 1.050000e-76 298.0
34 TraesCS3B01G120000 chr7D 78.778 311 48 11 1896 2205 406807848 406807555 5.080000e-45 193.0
35 TraesCS3B01G120000 chr1B 81.860 215 39 0 1981 2195 628030342 628030556 1.100000e-41 182.0
36 TraesCS3B01G120000 chr1B 96.364 55 1 1 3704 3757 544715349 544715295 6.860000e-14 89.8
37 TraesCS3B01G120000 chr1B 94.828 58 2 1 3704 3760 675255055 675254998 6.860000e-14 89.8
38 TraesCS3B01G120000 chr1B 91.935 62 4 1 3697 3757 210180404 210180465 8.880000e-13 86.1
39 TraesCS3B01G120000 chr6A 77.346 309 52 10 1898 2205 617707104 617706813 3.080000e-37 167.0
40 TraesCS3B01G120000 chr1D 90.805 87 6 1 1348 1432 375779691 375779777 1.130000e-21 115.0
41 TraesCS3B01G120000 chr6D 98.077 52 0 1 3704 3755 316281819 316281869 6.860000e-14 89.8
42 TraesCS3B01G120000 chr6B 96.364 55 1 1 3704 3757 713501252 713501306 6.860000e-14 89.8
43 TraesCS3B01G120000 chr2B 96.364 55 1 1 3704 3757 53244848 53244794 6.860000e-14 89.8
44 TraesCS3B01G120000 chr2B 83.582 67 8 3 87 153 137861147 137861210 5.380000e-05 60.2
45 TraesCS3B01G120000 chr5D 87.500 64 7 1 100 162 346703634 346703697 6.910000e-09 73.1
46 TraesCS3B01G120000 chr2A 83.077 65 6 3 87 151 86276255 86276314 3.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G120000 chr3B 90111950 90116926 4976 False 9191.000000 9191 100.000000 1 4977 1 chr3B.!!$F1 4976
1 TraesCS3B01G120000 chr3B 89609694 89611355 1661 False 784.500000 1271 84.599500 2362 4081 2 chr3B.!!$F5 1719
2 TraesCS3B01G120000 chr3B 89583902 89585921 2019 False 340.525000 747 91.173250 890 2359 4 chr3B.!!$F4 1469
3 TraesCS3B01G120000 chr3B 89626407 89627400 993 False 307.333333 322 87.258333 3110 4081 3 chr3B.!!$F6 971
4 TraesCS3B01G120000 chr3A 66216375 66226583 10208 False 1287.085714 4357 88.163429 447 4941 7 chr3A.!!$F1 4494
5 TraesCS3B01G120000 chr3D 57150924 57160151 9227 False 1059.700000 2444 91.672000 110 4922 6 chr3D.!!$F1 4812
6 TraesCS3B01G120000 chr3D 56846448 56850673 4225 True 728.750000 1240 87.061250 890 4217 4 chr3D.!!$R1 3327
7 TraesCS3B01G120000 chr4A 609324307 609325968 1661 False 784.500000 1271 84.599500 2362 4081 2 chr4A.!!$F1 1719
8 TraesCS3B01G120000 chr4A 609343581 609344574 993 False 307.333333 322 87.258333 3110 4081 3 chr4A.!!$F2 971

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
242 282 0.030101 CGGCGGTGCTTCTTCAAAAA 59.970 50.0 0.0 0.0 0.00 1.94 F
1565 2057 0.249657 GGTCGATGGAGTGGATCTGC 60.250 60.0 0.0 0.0 35.00 4.26 F
2585 5056 0.106521 GCCTGCATTTGGGTGTGTTT 59.893 50.0 0.0 0.0 0.00 2.83 F
3358 5948 0.106268 TGGCAGCTTTCAGGTTCCAA 60.106 50.0 0.0 0.0 36.15 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 4465 0.394352 CAGGATGGCGGCTAAAGGTT 60.394 55.0 11.43 0.0 0.00 3.50 R
3047 5595 1.203237 ATCGGTGACACATCATGGGA 58.797 50.0 8.08 0.0 37.14 4.37 R
3725 9665 1.064825 TTCAGGTGGGGAGTCTTTCC 58.935 55.0 0.00 0.0 46.00 3.13 R
4950 16581 0.512952 CGCCAGAAACGACCTTGAAG 59.487 55.0 0.00 0.0 0.00 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.809446 GCTTTTCAGTTTTCGCTTGGT 58.191 42.857 0.00 0.00 0.00 3.67
21 22 3.186909 GCTTTTCAGTTTTCGCTTGGTT 58.813 40.909 0.00 0.00 0.00 3.67
22 23 3.616821 GCTTTTCAGTTTTCGCTTGGTTT 59.383 39.130 0.00 0.00 0.00 3.27
23 24 4.092821 GCTTTTCAGTTTTCGCTTGGTTTT 59.907 37.500 0.00 0.00 0.00 2.43
24 25 5.723951 GCTTTTCAGTTTTCGCTTGGTTTTC 60.724 40.000 0.00 0.00 0.00 2.29
25 26 4.712122 TTCAGTTTTCGCTTGGTTTTCT 57.288 36.364 0.00 0.00 0.00 2.52
26 27 4.712122 TCAGTTTTCGCTTGGTTTTCTT 57.288 36.364 0.00 0.00 0.00 2.52
27 28 5.821516 TCAGTTTTCGCTTGGTTTTCTTA 57.178 34.783 0.00 0.00 0.00 2.10
28 29 5.816919 TCAGTTTTCGCTTGGTTTTCTTAG 58.183 37.500 0.00 0.00 0.00 2.18
29 30 4.976116 CAGTTTTCGCTTGGTTTTCTTAGG 59.024 41.667 0.00 0.00 0.00 2.69
30 31 4.643334 AGTTTTCGCTTGGTTTTCTTAGGT 59.357 37.500 0.00 0.00 0.00 3.08
31 32 5.126545 AGTTTTCGCTTGGTTTTCTTAGGTT 59.873 36.000 0.00 0.00 0.00 3.50
32 33 5.585820 TTTCGCTTGGTTTTCTTAGGTTT 57.414 34.783 0.00 0.00 0.00 3.27
33 34 5.585820 TTCGCTTGGTTTTCTTAGGTTTT 57.414 34.783 0.00 0.00 0.00 2.43
34 35 4.927422 TCGCTTGGTTTTCTTAGGTTTTG 58.073 39.130 0.00 0.00 0.00 2.44
35 36 4.641094 TCGCTTGGTTTTCTTAGGTTTTGA 59.359 37.500 0.00 0.00 0.00 2.69
36 37 5.125739 TCGCTTGGTTTTCTTAGGTTTTGAA 59.874 36.000 0.00 0.00 0.00 2.69
37 38 5.458779 CGCTTGGTTTTCTTAGGTTTTGAAG 59.541 40.000 0.00 0.00 0.00 3.02
38 39 6.338146 GCTTGGTTTTCTTAGGTTTTGAAGT 58.662 36.000 0.00 0.00 0.00 3.01
39 40 6.816640 GCTTGGTTTTCTTAGGTTTTGAAGTT 59.183 34.615 0.00 0.00 0.00 2.66
40 41 7.333423 GCTTGGTTTTCTTAGGTTTTGAAGTTT 59.667 33.333 0.00 0.00 0.00 2.66
41 42 9.214957 CTTGGTTTTCTTAGGTTTTGAAGTTTT 57.785 29.630 0.00 0.00 0.00 2.43
42 43 9.562408 TTGGTTTTCTTAGGTTTTGAAGTTTTT 57.438 25.926 0.00 0.00 0.00 1.94
71 72 4.536364 CGAAGCTTCTTGTGAAAGAACA 57.464 40.909 23.50 0.00 35.20 3.18
72 73 5.100751 CGAAGCTTCTTGTGAAAGAACAT 57.899 39.130 23.50 0.00 35.20 2.71
73 74 6.228273 CGAAGCTTCTTGTGAAAGAACATA 57.772 37.500 23.50 0.00 35.20 2.29
74 75 6.835914 CGAAGCTTCTTGTGAAAGAACATAT 58.164 36.000 23.50 0.00 35.20 1.78
75 76 7.301054 CGAAGCTTCTTGTGAAAGAACATATT 58.699 34.615 23.50 0.00 35.20 1.28
76 77 7.805071 CGAAGCTTCTTGTGAAAGAACATATTT 59.195 33.333 23.50 0.00 35.20 1.40
78 79 9.899226 AAGCTTCTTGTGAAAGAACATATTTAC 57.101 29.630 0.00 0.00 35.20 2.01
79 80 9.289782 AGCTTCTTGTGAAAGAACATATTTACT 57.710 29.630 0.00 0.00 35.20 2.24
80 81 9.899226 GCTTCTTGTGAAAGAACATATTTACTT 57.101 29.630 0.00 0.00 35.20 2.24
84 85 9.878599 CTTGTGAAAGAACATATTTACTTTCGT 57.121 29.630 0.00 0.00 46.05 3.85
85 86 9.658475 TTGTGAAAGAACATATTTACTTTCGTG 57.342 29.630 0.00 0.00 46.05 4.35
86 87 9.047371 TGTGAAAGAACATATTTACTTTCGTGA 57.953 29.630 0.00 0.00 46.05 4.35
90 91 9.825972 AAAGAACATATTTACTTTCGTGATGTG 57.174 29.630 0.00 0.00 0.00 3.21
91 92 7.464358 AGAACATATTTACTTTCGTGATGTGC 58.536 34.615 0.00 0.00 0.00 4.57
92 93 6.985188 ACATATTTACTTTCGTGATGTGCT 57.015 33.333 0.00 0.00 0.00 4.40
93 94 7.377766 ACATATTTACTTTCGTGATGTGCTT 57.622 32.000 0.00 0.00 0.00 3.91
94 95 7.464358 ACATATTTACTTTCGTGATGTGCTTC 58.536 34.615 0.00 0.00 0.00 3.86
95 96 7.334421 ACATATTTACTTTCGTGATGTGCTTCT 59.666 33.333 0.00 0.00 0.00 2.85
96 97 5.591643 TTTACTTTCGTGATGTGCTTCTC 57.408 39.130 0.00 0.00 0.00 2.87
97 98 2.061773 ACTTTCGTGATGTGCTTCTCG 58.938 47.619 4.05 4.05 34.77 4.04
98 99 1.391485 CTTTCGTGATGTGCTTCTCGG 59.609 52.381 8.78 0.00 34.37 4.63
99 100 0.389817 TTCGTGATGTGCTTCTCGGG 60.390 55.000 8.78 0.00 34.37 5.14
100 101 1.215382 CGTGATGTGCTTCTCGGGA 59.785 57.895 0.00 0.00 0.00 5.14
101 102 0.389817 CGTGATGTGCTTCTCGGGAA 60.390 55.000 0.00 0.00 0.00 3.97
102 103 1.808411 GTGATGTGCTTCTCGGGAAA 58.192 50.000 0.00 0.00 0.00 3.13
103 104 2.151202 GTGATGTGCTTCTCGGGAAAA 58.849 47.619 0.00 0.00 0.00 2.29
104 105 2.552315 GTGATGTGCTTCTCGGGAAAAA 59.448 45.455 0.00 0.00 0.00 1.94
159 160 0.874390 TCGTGGAAGCACAGATTTGC 59.126 50.000 0.00 0.00 43.34 3.68
176 177 1.522668 TGCTTATGCGAGTTGTGCTT 58.477 45.000 0.00 0.00 43.34 3.91
187 227 3.058914 CGAGTTGTGCTTCTCGGAAAAAT 60.059 43.478 6.67 0.00 46.26 1.82
192 232 4.778904 TGTGCTTCTCGGAAAAATAAACG 58.221 39.130 0.00 0.00 0.00 3.60
200 240 3.058085 TCGGAAAAATAAACGGTGCTTCC 60.058 43.478 0.00 0.00 0.00 3.46
204 244 2.172851 AATAAACGGTGCTTCCACGA 57.827 45.000 0.00 0.00 43.00 4.35
208 248 1.314730 AACGGTGCTTCCACGAAAAT 58.685 45.000 0.00 0.00 43.00 1.82
209 249 0.872388 ACGGTGCTTCCACGAAAATC 59.128 50.000 0.00 0.00 43.00 2.17
213 253 3.242413 CGGTGCTTCCACGAAAATCATAG 60.242 47.826 0.00 0.00 43.00 2.23
218 258 6.470235 GTGCTTCCACGAAAATCATAGATTTG 59.530 38.462 5.81 0.00 31.34 2.32
225 265 5.207768 CGAAAATCATAGATTTGCTTCCGG 58.792 41.667 5.81 0.00 0.00 5.14
226 266 4.574599 AAATCATAGATTTGCTTCCGGC 57.425 40.909 0.00 0.00 42.22 6.13
227 267 1.581934 TCATAGATTTGCTTCCGGCG 58.418 50.000 0.00 0.00 45.43 6.46
236 276 2.358737 CTTCCGGCGGTGCTTCTT 60.359 61.111 27.32 0.00 0.00 2.52
238 278 3.171828 TTCCGGCGGTGCTTCTTCA 62.172 57.895 27.32 0.00 0.00 3.02
239 279 2.668185 TTCCGGCGGTGCTTCTTCAA 62.668 55.000 27.32 6.30 0.00 2.69
240 280 2.258013 CCGGCGGTGCTTCTTCAAA 61.258 57.895 19.97 0.00 0.00 2.69
241 281 1.652012 CGGCGGTGCTTCTTCAAAA 59.348 52.632 0.00 0.00 0.00 2.44
242 282 0.030101 CGGCGGTGCTTCTTCAAAAA 59.970 50.000 0.00 0.00 0.00 1.94
294 335 0.319125 TTTGAAAATCGCAACCGGCC 60.319 50.000 0.00 0.00 40.31 6.13
332 374 9.774413 TTTTTCCTTTCTCTTTCTAGTATTCGT 57.226 29.630 0.00 0.00 0.00 3.85
333 375 8.758633 TTTCCTTTCTCTTTCTAGTATTCGTG 57.241 34.615 0.00 0.00 0.00 4.35
358 400 6.761731 TTTTTGCGAGAACATATTGTTTGG 57.238 33.333 0.00 0.00 41.28 3.28
359 401 5.446143 TTTGCGAGAACATATTGTTTGGT 57.554 34.783 0.00 0.00 41.28 3.67
361 403 5.041951 TGCGAGAACATATTGTTTGGTTC 57.958 39.130 0.00 0.00 41.28 3.62
395 437 7.856145 TTTGCACATATTTTGGTTTCTTTGT 57.144 28.000 0.00 0.00 0.00 2.83
396 438 7.856145 TTGCACATATTTTGGTTTCTTTGTT 57.144 28.000 0.00 0.00 0.00 2.83
397 439 7.856145 TGCACATATTTTGGTTTCTTTGTTT 57.144 28.000 0.00 0.00 0.00 2.83
398 440 8.273780 TGCACATATTTTGGTTTCTTTGTTTT 57.726 26.923 0.00 0.00 0.00 2.43
399 441 8.734386 TGCACATATTTTGGTTTCTTTGTTTTT 58.266 25.926 0.00 0.00 0.00 1.94
442 484 9.751542 TGTGAAGAAAAAGTTTGACAAAAACTA 57.248 25.926 1.27 0.00 39.36 2.24
459 501 9.289782 ACAAAAACTATAATCATGGGATCTAGC 57.710 33.333 0.00 0.00 31.88 3.42
461 503 9.732130 AAAAACTATAATCATGGGATCTAGCTC 57.268 33.333 0.00 0.00 31.88 4.09
463 505 5.596361 ACTATAATCATGGGATCTAGCTCCG 59.404 44.000 6.54 0.00 36.05 4.63
470 512 2.109128 TGGGATCTAGCTCCGAAGATCT 59.891 50.000 19.05 0.00 44.94 2.75
477 519 1.135257 AGCTCCGAAGATCTCAACACG 60.135 52.381 0.00 0.00 0.00 4.49
484 526 5.468746 TCCGAAGATCTCAACACGAAAAATT 59.531 36.000 0.00 0.00 0.00 1.82
488 530 7.535258 CGAAGATCTCAACACGAAAAATTCAAT 59.465 33.333 0.00 0.00 0.00 2.57
489 531 8.511465 AAGATCTCAACACGAAAAATTCAATG 57.489 30.769 0.00 0.00 0.00 2.82
514 556 8.303156 TGATGAAAACGATTTGGTATTTGACAT 58.697 29.630 0.00 0.00 0.00 3.06
515 557 9.781834 GATGAAAACGATTTGGTATTTGACATA 57.218 29.630 0.00 0.00 0.00 2.29
518 560 6.971527 AACGATTTGGTATTTGACATACGA 57.028 33.333 0.00 0.00 0.00 3.43
524 566 9.781834 GATTTGGTATTTGACATACGATTCAAA 57.218 29.630 0.00 0.00 43.89 2.69
525 567 9.787532 ATTTGGTATTTGACATACGATTCAAAG 57.212 29.630 0.00 0.00 43.21 2.77
560 602 7.901874 TTTGGAAAACGAATCTAGAAAAACG 57.098 32.000 0.00 3.26 0.00 3.60
583 626 6.181255 CGAGAAACTTTCATATTGCGAGAAG 58.819 40.000 4.34 0.00 0.00 2.85
598 655 1.001378 GAGAAGTGGCGCATTTGTTGT 60.001 47.619 10.83 0.00 0.00 3.32
616 673 4.141505 TGTTGTCAAATCAGAGAAGGTGGA 60.142 41.667 0.00 0.00 0.00 4.02
618 675 3.008375 TGTCAAATCAGAGAAGGTGGAGG 59.992 47.826 0.00 0.00 0.00 4.30
619 676 3.261897 GTCAAATCAGAGAAGGTGGAGGA 59.738 47.826 0.00 0.00 0.00 3.71
620 677 3.517100 TCAAATCAGAGAAGGTGGAGGAG 59.483 47.826 0.00 0.00 0.00 3.69
621 678 2.938428 ATCAGAGAAGGTGGAGGAGT 57.062 50.000 0.00 0.00 0.00 3.85
622 679 4.338795 AATCAGAGAAGGTGGAGGAGTA 57.661 45.455 0.00 0.00 0.00 2.59
634 691 4.321974 GGTGGAGGAGTAATTTTTGCAAGG 60.322 45.833 0.00 0.00 0.00 3.61
638 695 5.944007 GGAGGAGTAATTTTTGCAAGGAGTA 59.056 40.000 0.00 0.00 0.00 2.59
685 762 7.496747 TCATAAATACGACCATGATGTGAAGA 58.503 34.615 0.00 0.00 0.00 2.87
686 763 8.150296 TCATAAATACGACCATGATGTGAAGAT 58.850 33.333 0.00 0.00 0.00 2.40
815 893 2.815211 CGATGTGTCGCCACCAGG 60.815 66.667 0.00 0.00 41.49 4.45
876 959 2.159310 CCAACTTTTCCAAGCACGAACA 60.159 45.455 0.00 0.00 32.57 3.18
896 979 4.787280 CTCCCCTCCTCCACCGCT 62.787 72.222 0.00 0.00 0.00 5.52
943 1037 3.876255 AAACCGCCCTCCCTACCCA 62.876 63.158 0.00 0.00 0.00 4.51
944 1038 3.876255 AACCGCCCTCCCTACCCAA 62.876 63.158 0.00 0.00 0.00 4.12
1170 1272 2.047274 GGGTGCTGCAACGAGCTA 60.047 61.111 12.13 0.00 45.94 3.32
1172 1274 1.639298 GGGTGCTGCAACGAGCTAAG 61.639 60.000 12.13 0.00 45.94 2.18
1422 1524 0.249911 GCTTCCAGAACGTCACCTGT 60.250 55.000 10.36 0.00 0.00 4.00
1473 1868 5.469084 AGTTTTAATGTCGTTCCTCAAGACC 59.531 40.000 0.00 0.00 34.24 3.85
1489 1979 6.151648 CCTCAAGACCAAATGCTCTGATTTTA 59.848 38.462 0.00 0.00 0.00 1.52
1556 2048 3.403038 AGTTTCAGTTTGGTCGATGGAG 58.597 45.455 0.00 0.00 0.00 3.86
1565 2057 0.249657 GGTCGATGGAGTGGATCTGC 60.250 60.000 0.00 0.00 35.00 4.26
1576 2070 2.766263 AGTGGATCTGCGGTCTAATTCA 59.234 45.455 0.00 0.00 0.00 2.57
1588 2082 5.336451 GCGGTCTAATTCACAATTCCCTTTT 60.336 40.000 0.00 0.00 32.38 2.27
1589 2083 6.322491 CGGTCTAATTCACAATTCCCTTTTC 58.678 40.000 0.00 0.00 32.38 2.29
1636 2132 4.843728 TCTAATTGTTCCTCCATGTCCAC 58.156 43.478 0.00 0.00 0.00 4.02
1648 2144 2.093447 CCATGTCCACTAGTCTGGGTTC 60.093 54.545 0.00 0.00 31.41 3.62
1649 2145 2.391926 TGTCCACTAGTCTGGGTTCA 57.608 50.000 0.00 0.00 31.41 3.18
1662 2158 2.107552 CTGGGTTCAGGGGTTTAGTTGA 59.892 50.000 0.00 0.00 37.36 3.18
1665 2161 3.509967 GGGTTCAGGGGTTTAGTTGATTG 59.490 47.826 0.00 0.00 0.00 2.67
1671 2192 3.655777 AGGGGTTTAGTTGATTGTCAGGA 59.344 43.478 0.00 0.00 0.00 3.86
1675 2196 6.661805 GGGGTTTAGTTGATTGTCAGGAAATA 59.338 38.462 0.00 0.00 0.00 1.40
1679 2200 8.515414 GTTTAGTTGATTGTCAGGAAATAGCTT 58.485 33.333 0.00 0.00 0.00 3.74
1766 2460 7.451501 TCATACAATTTGCAATCTTGAGACA 57.548 32.000 22.18 9.54 0.00 3.41
1767 2461 8.058667 TCATACAATTTGCAATCTTGAGACAT 57.941 30.769 22.18 10.83 0.00 3.06
1768 2462 9.176460 TCATACAATTTGCAATCTTGAGACATA 57.824 29.630 22.18 9.33 0.00 2.29
1769 2463 9.791820 CATACAATTTGCAATCTTGAGACATAA 57.208 29.630 22.18 0.00 0.00 1.90
1772 2466 9.715121 ACAATTTGCAATCTTGAGACATAATTT 57.285 25.926 22.18 1.10 0.00 1.82
1825 3778 5.659440 TCCGCAGATGATATGTATGCTTA 57.341 39.130 3.66 0.00 34.75 3.09
1881 4295 6.541278 GGCAAGATATCTATATGAGCATTGCA 59.459 38.462 11.91 0.00 0.00 4.08
1883 4297 8.456471 GCAAGATATCTATATGAGCATTGCAAA 58.544 33.333 11.91 0.00 0.00 3.68
1941 4360 2.571212 CAGGCAGTGGTGAACAACTTA 58.429 47.619 0.00 0.00 0.00 2.24
1965 4384 4.533815 AGGATGCACATGAACAGATTGAT 58.466 39.130 0.00 0.00 0.00 2.57
1976 4395 6.198650 TGAACAGATTGATACTGCCATTTG 57.801 37.500 0.00 0.00 38.74 2.32
2046 4465 3.233980 CCCTCGATCCCGCATCCA 61.234 66.667 0.00 0.00 35.37 3.41
2114 4533 1.218047 GCATGCTCCCTGTACACGA 59.782 57.895 11.37 0.00 0.00 4.35
2123 4542 5.105269 TGCTCCCTGTACACGAATAACAATA 60.105 40.000 0.00 0.00 0.00 1.90
2150 4621 3.380471 TGGCAGTTGGCTTGGTATTAT 57.620 42.857 7.23 0.00 44.01 1.28
2156 4627 5.284079 CAGTTGGCTTGGTATTATTGATGC 58.716 41.667 0.00 0.00 0.00 3.91
2167 4638 6.016860 TGGTATTATTGATGCTGATGAACTGC 60.017 38.462 0.00 0.00 42.47 4.40
2173 4644 3.377172 TGATGCTGATGAACTGCTCATTG 59.623 43.478 0.00 0.00 45.23 2.82
2185 4656 1.973515 TGCTCATTGGTCAGACTGTCT 59.026 47.619 4.06 4.06 0.00 3.41
2291 4762 0.899717 GATGAGGGTGGCCAAAGCAA 60.900 55.000 7.24 0.00 42.56 3.91
2450 4921 3.262660 TGAGATTGTGGAGTCAGCTGATT 59.737 43.478 21.47 16.77 0.00 2.57
2509 4980 0.458025 CGGTTGGGTACTCGCTTCTC 60.458 60.000 0.00 0.00 0.00 2.87
2541 5012 0.333993 AAGGCCATCATTGTCCAGCT 59.666 50.000 5.01 0.00 0.00 4.24
2585 5056 0.106521 GCCTGCATTTGGGTGTGTTT 59.893 50.000 0.00 0.00 0.00 2.83
2608 5079 0.674581 TGAAGGACTTCCTGCATGCG 60.675 55.000 14.09 7.87 46.73 4.73
2927 5469 7.094975 TGGTCACATCCGTTCTTTTAGTATTTG 60.095 37.037 0.00 0.00 0.00 2.32
3023 5570 7.440255 GGGAGAATTTGATAAAAATGCCTCATG 59.560 37.037 11.90 0.00 0.00 3.07
3043 5591 7.495934 CCTCATGGTAGTTTGAACTTCGATAAT 59.504 37.037 1.20 0.00 40.37 1.28
3087 5666 7.093727 ACCGATTAGTGAGGTCATATTATCAGG 60.094 40.741 0.00 0.00 31.69 3.86
3094 5673 6.260936 GTGAGGTCATATTATCAGGTGGTTTG 59.739 42.308 0.00 0.00 0.00 2.93
3114 5702 9.567776 TGGTTTGATGTAAGAGTCTCAAAAATA 57.432 29.630 1.94 0.00 38.81 1.40
3198 5788 8.900781 TCAGTAAGTAGGATGTATACTGTTCAC 58.099 37.037 4.17 0.00 42.44 3.18
3312 5902 3.198489 GCGCAGGCTGCTAAGGAC 61.198 66.667 34.17 14.40 42.25 3.85
3354 5944 1.615384 GGAGATGGCAGCTTTCAGGTT 60.615 52.381 6.75 0.00 0.00 3.50
3356 5946 0.813821 GATGGCAGCTTTCAGGTTCC 59.186 55.000 0.00 0.00 29.55 3.62
3357 5947 0.112995 ATGGCAGCTTTCAGGTTCCA 59.887 50.000 0.00 0.00 42.72 3.53
3358 5948 0.106268 TGGCAGCTTTCAGGTTCCAA 60.106 50.000 0.00 0.00 36.15 3.53
3359 5949 1.039856 GGCAGCTTTCAGGTTCCAAA 58.960 50.000 0.00 0.00 29.33 3.28
3385 5978 7.642071 AAAATTCAGAATCACCAAATGTTCG 57.358 32.000 0.00 0.00 0.00 3.95
3395 5988 8.964476 AATCACCAAATGTTCGATCTTATACT 57.036 30.769 0.00 0.00 0.00 2.12
3724 9664 1.394618 TTTTGAAACTGTCACCCGGG 58.605 50.000 22.25 22.25 35.39 5.73
3725 9665 0.466555 TTTGAAACTGTCACCCGGGG 60.467 55.000 27.92 12.73 35.39 5.73
3752 9692 6.441088 AGACTCCCCACCTGAATATATTTC 57.559 41.667 0.00 0.00 0.00 2.17
3796 9736 5.048573 GCATTGCAATGAAATTTCACCCTTT 60.049 36.000 37.36 10.62 40.49 3.11
3982 9924 1.176527 CAAATCCCCAGTGAACGCAT 58.823 50.000 0.00 0.00 0.00 4.73
4082 10025 2.019984 GATCCATTTGAGTCCACTGCC 58.980 52.381 0.00 0.00 0.00 4.85
4235 15491 3.518634 TTTTGACAACAGTTTCAGGCC 57.481 42.857 0.00 0.00 0.00 5.19
4253 15509 3.513515 AGGCCTGTTGTGTTTCTCAAAAA 59.486 39.130 3.11 0.00 0.00 1.94
4261 15517 8.459521 TGTTGTGTTTCTCAAAAACATTAGTG 57.540 30.769 6.62 0.00 41.51 2.74
4273 15529 8.237949 TCAAAAACATTAGTGAGACGAAACAAA 58.762 29.630 0.00 0.00 0.00 2.83
4318 15574 8.641498 AGAAGATTCAATTATGTGGTGAAGTT 57.359 30.769 0.00 0.00 34.91 2.66
4319 15575 9.082313 AGAAGATTCAATTATGTGGTGAAGTTT 57.918 29.630 0.00 0.00 34.91 2.66
4322 15578 9.520515 AGATTCAATTATGTGGTGAAGTTTACT 57.479 29.630 0.00 0.00 34.91 2.24
4323 15579 9.559958 GATTCAATTATGTGGTGAAGTTTACTG 57.440 33.333 0.00 0.00 34.91 2.74
4324 15580 8.684386 TTCAATTATGTGGTGAAGTTTACTGA 57.316 30.769 0.00 0.00 0.00 3.41
4325 15581 8.684386 TCAATTATGTGGTGAAGTTTACTGAA 57.316 30.769 0.00 0.00 0.00 3.02
4326 15582 9.295825 TCAATTATGTGGTGAAGTTTACTGAAT 57.704 29.630 0.00 0.00 0.00 2.57
4327 15583 9.345517 CAATTATGTGGTGAAGTTTACTGAATG 57.654 33.333 0.00 0.00 0.00 2.67
4328 15584 8.635765 ATTATGTGGTGAAGTTTACTGAATGT 57.364 30.769 0.00 0.00 0.00 2.71
4329 15585 6.560253 ATGTGGTGAAGTTTACTGAATGTC 57.440 37.500 0.00 0.00 0.00 3.06
4330 15586 5.432645 TGTGGTGAAGTTTACTGAATGTCA 58.567 37.500 0.00 0.00 0.00 3.58
4331 15587 5.883115 TGTGGTGAAGTTTACTGAATGTCAA 59.117 36.000 0.00 0.00 0.00 3.18
4332 15588 6.375736 TGTGGTGAAGTTTACTGAATGTCAAA 59.624 34.615 0.00 0.00 0.00 2.69
4333 15589 7.094162 TGTGGTGAAGTTTACTGAATGTCAAAA 60.094 33.333 0.00 0.00 0.00 2.44
4334 15590 7.220108 GTGGTGAAGTTTACTGAATGTCAAAAC 59.780 37.037 0.00 0.00 30.95 2.43
4335 15591 7.094162 TGGTGAAGTTTACTGAATGTCAAAACA 60.094 33.333 7.79 0.00 40.38 2.83
4336 15592 7.757624 GGTGAAGTTTACTGAATGTCAAAACAA 59.242 33.333 7.79 0.00 39.30 2.83
4337 15593 9.134734 GTGAAGTTTACTGAATGTCAAAACAAA 57.865 29.630 7.79 0.00 39.30 2.83
4338 15594 9.868277 TGAAGTTTACTGAATGTCAAAACAAAT 57.132 25.926 7.79 0.00 39.30 2.32
4341 15597 8.603181 AGTTTACTGAATGTCAAAACAAATTGC 58.397 29.630 0.00 0.00 39.30 3.56
4342 15598 8.386606 GTTTACTGAATGTCAAAACAAATTGCA 58.613 29.630 0.00 0.00 39.30 4.08
4343 15599 6.981762 ACTGAATGTCAAAACAAATTGCAA 57.018 29.167 0.00 0.00 39.30 4.08
4344 15600 7.556733 ACTGAATGTCAAAACAAATTGCAAT 57.443 28.000 5.99 5.99 39.30 3.56
4345 15601 7.411274 ACTGAATGTCAAAACAAATTGCAATG 58.589 30.769 13.82 5.51 39.30 2.82
4346 15602 7.280428 ACTGAATGTCAAAACAAATTGCAATGA 59.720 29.630 13.82 2.29 39.30 2.57
4347 15603 7.982224 TGAATGTCAAAACAAATTGCAATGAA 58.018 26.923 13.82 0.00 39.30 2.57
4357 15614 7.789273 ACAAATTGCAATGAAAACTCAATGA 57.211 28.000 13.82 0.00 0.00 2.57
4366 15623 3.507233 TGAAAACTCAATGATGCACTCCC 59.493 43.478 0.00 0.00 0.00 4.30
4367 15624 2.885135 AACTCAATGATGCACTCCCA 57.115 45.000 0.00 0.00 0.00 4.37
4507 15769 5.921962 AAAAGGTTTCAGTGCTCTTTTCT 57.078 34.783 0.00 0.00 33.92 2.52
4544 15806 8.344446 ACATAGGTGTAAAGAAAATTGGTACC 57.656 34.615 4.43 4.43 36.63 3.34
4545 15807 8.168058 ACATAGGTGTAAAGAAAATTGGTACCT 58.832 33.333 14.36 0.00 36.63 3.08
4546 15808 9.675464 CATAGGTGTAAAGAAAATTGGTACCTA 57.325 33.333 14.36 5.86 41.08 3.08
4609 16238 8.594550 TCACATCTCTACCTAATATTAAAGGGC 58.405 37.037 8.77 0.00 37.18 5.19
4610 16239 8.598041 CACATCTCTACCTAATATTAAAGGGCT 58.402 37.037 8.77 0.00 37.18 5.19
4683 16312 6.708054 CCTAATATTAAAGGGAGCTGTCTGTG 59.292 42.308 0.00 0.00 0.00 3.66
4765 16394 6.128035 GGAAAGTGGCAGTTTTCAAAATGTTT 60.128 34.615 20.50 0.00 36.45 2.83
4907 16538 7.168637 CGGCCAATTCTAAGATTGATGAATTTG 59.831 37.037 2.24 0.00 38.93 2.32
4918 16549 2.633967 TGATGAATTTGGGCTGCTGTTT 59.366 40.909 0.00 0.00 0.00 2.83
4942 16573 0.528924 GCATCAATTGGACAGCAGCA 59.471 50.000 5.42 0.00 31.94 4.41
4944 16575 2.876091 CATCAATTGGACAGCAGCAAG 58.124 47.619 5.42 0.00 0.00 4.01
4946 16577 0.963962 CAATTGGACAGCAGCAAGGT 59.036 50.000 0.00 0.00 0.00 3.50
4947 16578 1.068055 CAATTGGACAGCAGCAAGGTC 60.068 52.381 0.00 0.00 0.00 3.85
4949 16580 2.753029 GGACAGCAGCAAGGTCCT 59.247 61.111 18.70 0.00 45.99 3.85
4950 16581 1.376553 GGACAGCAGCAAGGTCCTC 60.377 63.158 18.70 0.02 45.99 3.71
4951 16582 1.676384 GACAGCAGCAAGGTCCTCT 59.324 57.895 0.00 0.00 0.00 3.69
4952 16583 0.036022 GACAGCAGCAAGGTCCTCTT 59.964 55.000 0.00 0.00 35.79 2.85
4953 16584 0.036022 ACAGCAGCAAGGTCCTCTTC 59.964 55.000 0.00 0.00 32.41 2.87
4954 16585 0.035881 CAGCAGCAAGGTCCTCTTCA 59.964 55.000 0.00 0.00 32.41 3.02
4955 16586 0.767375 AGCAGCAAGGTCCTCTTCAA 59.233 50.000 0.00 0.00 32.41 2.69
4956 16587 1.163554 GCAGCAAGGTCCTCTTCAAG 58.836 55.000 0.00 0.00 32.41 3.02
4958 16589 1.072965 CAGCAAGGTCCTCTTCAAGGT 59.927 52.381 0.00 0.00 46.32 3.50
4959 16590 1.349357 AGCAAGGTCCTCTTCAAGGTC 59.651 52.381 0.00 0.00 46.32 3.85
4960 16591 1.941668 GCAAGGTCCTCTTCAAGGTCG 60.942 57.143 0.00 0.00 46.32 4.79
4961 16592 1.344763 CAAGGTCCTCTTCAAGGTCGT 59.655 52.381 0.00 0.00 46.32 4.34
4962 16593 1.718280 AGGTCCTCTTCAAGGTCGTT 58.282 50.000 0.00 0.00 46.32 3.85
4963 16594 2.047830 AGGTCCTCTTCAAGGTCGTTT 58.952 47.619 0.00 0.00 46.32 3.60
4964 16595 2.037381 AGGTCCTCTTCAAGGTCGTTTC 59.963 50.000 0.00 0.00 46.32 2.78
4965 16596 2.037381 GGTCCTCTTCAAGGTCGTTTCT 59.963 50.000 0.00 0.00 46.32 2.52
4966 16597 3.060602 GTCCTCTTCAAGGTCGTTTCTG 58.939 50.000 0.00 0.00 46.32 3.02
4967 16598 2.037251 TCCTCTTCAAGGTCGTTTCTGG 59.963 50.000 0.00 0.00 46.32 3.86
4968 16599 1.801178 CTCTTCAAGGTCGTTTCTGGC 59.199 52.381 0.00 0.00 0.00 4.85
4969 16600 0.512952 CTTCAAGGTCGTTTCTGGCG 59.487 55.000 0.00 0.00 0.00 5.69
4970 16601 1.503818 TTCAAGGTCGTTTCTGGCGC 61.504 55.000 0.00 0.00 0.00 6.53
4971 16602 2.110213 AAGGTCGTTTCTGGCGCA 59.890 55.556 10.83 0.00 0.00 6.09
4972 16603 2.251642 AAGGTCGTTTCTGGCGCAC 61.252 57.895 10.83 0.00 0.00 5.34
4973 16604 3.723348 GGTCGTTTCTGGCGCACC 61.723 66.667 10.83 0.65 0.00 5.01
4974 16605 4.072088 GTCGTTTCTGGCGCACCG 62.072 66.667 10.83 1.21 39.70 4.94
4975 16606 4.287781 TCGTTTCTGGCGCACCGA 62.288 61.111 10.83 3.88 39.70 4.69
4976 16607 4.072088 CGTTTCTGGCGCACCGAC 62.072 66.667 10.83 0.00 39.70 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.809446 ACCAAGCGAAAACTGAAAAGC 58.191 42.857 0.00 0.00 0.00 3.51
1 2 5.576774 AGAAAACCAAGCGAAAACTGAAAAG 59.423 36.000 0.00 0.00 0.00 2.27
2 3 5.474825 AGAAAACCAAGCGAAAACTGAAAA 58.525 33.333 0.00 0.00 0.00 2.29
3 4 5.066968 AGAAAACCAAGCGAAAACTGAAA 57.933 34.783 0.00 0.00 0.00 2.69
4 5 4.712122 AGAAAACCAAGCGAAAACTGAA 57.288 36.364 0.00 0.00 0.00 3.02
5 6 4.712122 AAGAAAACCAAGCGAAAACTGA 57.288 36.364 0.00 0.00 0.00 3.41
6 7 4.976116 CCTAAGAAAACCAAGCGAAAACTG 59.024 41.667 0.00 0.00 0.00 3.16
7 8 4.643334 ACCTAAGAAAACCAAGCGAAAACT 59.357 37.500 0.00 0.00 0.00 2.66
8 9 4.928601 ACCTAAGAAAACCAAGCGAAAAC 58.071 39.130 0.00 0.00 0.00 2.43
9 10 5.585820 AACCTAAGAAAACCAAGCGAAAA 57.414 34.783 0.00 0.00 0.00 2.29
10 11 5.585820 AAACCTAAGAAAACCAAGCGAAA 57.414 34.783 0.00 0.00 0.00 3.46
11 12 5.125739 TCAAAACCTAAGAAAACCAAGCGAA 59.874 36.000 0.00 0.00 0.00 4.70
12 13 4.641094 TCAAAACCTAAGAAAACCAAGCGA 59.359 37.500 0.00 0.00 0.00 4.93
13 14 4.927422 TCAAAACCTAAGAAAACCAAGCG 58.073 39.130 0.00 0.00 0.00 4.68
14 15 6.338146 ACTTCAAAACCTAAGAAAACCAAGC 58.662 36.000 0.00 0.00 0.00 4.01
15 16 8.771920 AAACTTCAAAACCTAAGAAAACCAAG 57.228 30.769 0.00 0.00 0.00 3.61
16 17 9.562408 AAAAACTTCAAAACCTAAGAAAACCAA 57.438 25.926 0.00 0.00 0.00 3.67
44 45 3.773860 TCACAAGAAGCTTCGCAAAAA 57.226 38.095 20.43 3.83 0.00 1.94
45 46 3.773860 TTCACAAGAAGCTTCGCAAAA 57.226 38.095 20.43 9.93 0.00 2.44
46 47 3.376859 TCTTTCACAAGAAGCTTCGCAAA 59.623 39.130 20.43 13.77 35.99 3.68
47 48 2.942376 TCTTTCACAAGAAGCTTCGCAA 59.058 40.909 20.43 7.51 35.99 4.85
48 49 2.560504 TCTTTCACAAGAAGCTTCGCA 58.439 42.857 20.43 1.59 35.99 5.10
49 50 3.609103 TTCTTTCACAAGAAGCTTCGC 57.391 42.857 20.43 0.00 42.99 4.70
58 59 9.878599 ACGAAAGTAAATATGTTCTTTCACAAG 57.121 29.630 19.36 9.49 46.88 3.16
78 79 1.391485 CCGAGAAGCACATCACGAAAG 59.609 52.381 0.00 0.00 35.78 2.62
79 80 1.428448 CCGAGAAGCACATCACGAAA 58.572 50.000 0.00 0.00 35.78 3.46
80 81 0.389817 CCCGAGAAGCACATCACGAA 60.390 55.000 0.00 0.00 35.78 3.85
81 82 1.215382 CCCGAGAAGCACATCACGA 59.785 57.895 0.00 0.00 35.78 4.35
82 83 0.389817 TTCCCGAGAAGCACATCACG 60.390 55.000 0.00 0.00 33.93 4.35
83 84 1.808411 TTTCCCGAGAAGCACATCAC 58.192 50.000 0.00 0.00 32.35 3.06
84 85 2.559698 TTTTCCCGAGAAGCACATCA 57.440 45.000 0.00 0.00 32.35 3.07
151 152 4.093514 CACAACTCGCATAAGCAAATCTG 58.906 43.478 0.00 0.00 42.27 2.90
159 160 2.028523 CGAGAAGCACAACTCGCATAAG 59.971 50.000 0.00 0.00 46.54 1.73
162 163 2.449548 CGAGAAGCACAACTCGCAT 58.550 52.632 0.00 0.00 46.54 4.73
163 164 3.936653 CGAGAAGCACAACTCGCA 58.063 55.556 0.00 0.00 46.54 5.10
176 177 3.404899 AGCACCGTTTATTTTTCCGAGA 58.595 40.909 0.00 0.00 0.00 4.04
180 181 3.985279 GTGGAAGCACCGTTTATTTTTCC 59.015 43.478 0.00 0.00 42.61 3.13
187 227 1.950828 TTTCGTGGAAGCACCGTTTA 58.049 45.000 0.00 0.00 42.61 2.01
192 232 3.938963 TCTATGATTTTCGTGGAAGCACC 59.061 43.478 0.00 0.00 39.54 5.01
200 240 5.678483 CGGAAGCAAATCTATGATTTTCGTG 59.322 40.000 3.13 0.00 0.00 4.35
204 244 4.498009 CGCCGGAAGCAAATCTATGATTTT 60.498 41.667 5.05 0.00 44.04 1.82
208 248 1.581934 CGCCGGAAGCAAATCTATGA 58.418 50.000 5.05 0.00 44.04 2.15
209 249 0.588252 CCGCCGGAAGCAAATCTATG 59.412 55.000 5.05 0.00 44.04 2.23
213 253 2.485122 CACCGCCGGAAGCAAATC 59.515 61.111 11.71 0.00 44.04 2.17
291 332 1.379146 AAAAAGGAGACGGGAGGCC 59.621 57.895 0.00 0.00 40.49 5.19
372 414 7.856145 AACAAAGAAACCAAAATATGTGCAA 57.144 28.000 0.00 0.00 0.00 4.08
373 415 7.856145 AAACAAAGAAACCAAAATATGTGCA 57.144 28.000 0.00 0.00 0.00 4.57
430 472 9.699410 AGATCCCATGATTATAGTTTTTGTCAA 57.301 29.630 0.00 0.00 0.00 3.18
433 475 9.289782 GCTAGATCCCATGATTATAGTTTTTGT 57.710 33.333 0.00 0.00 0.00 2.83
439 481 5.596361 CGGAGCTAGATCCCATGATTATAGT 59.404 44.000 21.17 0.00 35.82 2.12
442 484 4.614475 TCGGAGCTAGATCCCATGATTAT 58.386 43.478 21.17 0.00 35.82 1.28
449 491 2.109128 AGATCTTCGGAGCTAGATCCCA 59.891 50.000 21.17 5.74 42.37 4.37
459 501 2.921634 TCGTGTTGAGATCTTCGGAG 57.078 50.000 0.00 0.00 0.00 4.63
461 503 4.725556 TTTTTCGTGTTGAGATCTTCGG 57.274 40.909 0.00 0.00 0.00 4.30
463 505 8.633408 CATTGAATTTTTCGTGTTGAGATCTTC 58.367 33.333 0.00 0.00 0.00 2.87
470 512 8.640091 TTTCATCATTGAATTTTTCGTGTTGA 57.360 26.923 0.00 0.00 41.38 3.18
484 526 9.138062 CAAATACCAAATCGTTTTCATCATTGA 57.862 29.630 0.00 0.00 0.00 2.57
488 530 7.652727 TGTCAAATACCAAATCGTTTTCATCA 58.347 30.769 0.00 0.00 0.00 3.07
489 531 8.687824 ATGTCAAATACCAAATCGTTTTCATC 57.312 30.769 0.00 0.00 0.00 2.92
498 540 9.781834 TTTGAATCGTATGTCAAATACCAAATC 57.218 29.630 0.00 0.00 38.50 2.17
499 541 9.787532 CTTTGAATCGTATGTCAAATACCAAAT 57.212 29.630 0.00 0.00 41.57 2.32
534 576 8.964150 CGTTTTTCTAGATTCGTTTTCCAAAAT 58.036 29.630 0.00 0.00 0.00 1.82
539 581 7.113704 TCTCGTTTTTCTAGATTCGTTTTCC 57.886 36.000 0.00 0.00 0.00 3.13
540 582 8.880265 GTTTCTCGTTTTTCTAGATTCGTTTTC 58.120 33.333 0.00 0.00 0.00 2.29
545 587 8.273557 TGAAAGTTTCTCGTTTTTCTAGATTCG 58.726 33.333 16.33 0.00 32.28 3.34
559 601 5.702622 TCTCGCAATATGAAAGTTTCTCG 57.297 39.130 16.33 9.80 0.00 4.04
560 602 6.958193 CACTTCTCGCAATATGAAAGTTTCTC 59.042 38.462 16.33 0.00 0.00 2.87
583 626 1.565305 TTTGACAACAAATGCGCCAC 58.435 45.000 4.18 0.00 40.47 5.01
598 655 3.517100 CTCCTCCACCTTCTCTGATTTGA 59.483 47.826 0.00 0.00 0.00 2.69
605 662 6.241645 CAAAAATTACTCCTCCACCTTCTCT 58.758 40.000 0.00 0.00 0.00 3.10
612 669 4.522789 TCCTTGCAAAAATTACTCCTCCAC 59.477 41.667 0.00 0.00 0.00 4.02
613 670 4.735369 TCCTTGCAAAAATTACTCCTCCA 58.265 39.130 0.00 0.00 0.00 3.86
616 673 6.603599 GGATACTCCTTGCAAAAATTACTCCT 59.396 38.462 0.00 0.00 32.53 3.69
634 691 6.761099 TCACTAGTCAAGTCAAGGATACTC 57.239 41.667 0.00 0.00 41.92 2.59
638 695 7.009179 TGAAATCACTAGTCAAGTCAAGGAT 57.991 36.000 0.00 0.00 35.76 3.24
668 725 3.273434 CCAATCTTCACATCATGGTCGT 58.727 45.455 0.00 0.00 0.00 4.34
685 762 8.094548 GCCCAACTTTAGAAATTAAAGACCAAT 58.905 33.333 12.23 0.00 37.80 3.16
686 763 7.438564 GCCCAACTTTAGAAATTAAAGACCAA 58.561 34.615 12.23 0.00 37.80 3.67
810 888 2.883828 CGGACAGTTGGAGCCTGGT 61.884 63.158 0.00 0.00 34.16 4.00
812 890 1.374758 GTCGGACAGTTGGAGCCTG 60.375 63.158 2.62 0.00 36.01 4.85
813 891 2.932234 CGTCGGACAGTTGGAGCCT 61.932 63.158 9.10 0.00 0.00 4.58
814 892 2.432628 CGTCGGACAGTTGGAGCC 60.433 66.667 9.10 0.00 0.00 4.70
815 893 3.112709 GCGTCGGACAGTTGGAGC 61.113 66.667 9.10 0.00 0.00 4.70
876 959 1.383248 CGGTGGAGGAGGGGAGAAT 60.383 63.158 0.00 0.00 0.00 2.40
927 1021 4.342086 TTGGGTAGGGAGGGCGGT 62.342 66.667 0.00 0.00 0.00 5.68
1059 1161 2.014554 CACGGTGAAGACGTCGTGG 61.015 63.158 9.23 0.00 46.05 4.94
1061 1163 2.354305 GCACGGTGAAGACGTCGT 60.354 61.111 13.29 6.85 43.58 4.34
1422 1524 5.942236 ACAACAGAGACGTACTACCTGATAA 59.058 40.000 0.00 0.00 0.00 1.75
1489 1979 3.105959 AGCAGTGCCAAAATCCCTAAT 57.894 42.857 12.58 0.00 0.00 1.73
1541 2033 1.348064 TCCACTCCATCGACCAAACT 58.652 50.000 0.00 0.00 0.00 2.66
1556 2048 2.866762 GTGAATTAGACCGCAGATCCAC 59.133 50.000 0.00 0.00 0.00 4.02
1565 2057 5.897377 AAAGGGAATTGTGAATTAGACCG 57.103 39.130 0.00 0.00 0.00 4.79
1576 2070 5.598005 TGAACATGTCAGAAAAGGGAATTGT 59.402 36.000 0.00 0.00 0.00 2.71
1636 2132 1.657804 AACCCCTGAACCCAGACTAG 58.342 55.000 0.00 0.00 43.02 2.57
1648 2144 3.758554 CCTGACAATCAACTAAACCCCTG 59.241 47.826 0.00 0.00 0.00 4.45
1649 2145 3.655777 TCCTGACAATCAACTAAACCCCT 59.344 43.478 0.00 0.00 0.00 4.79
1662 2158 4.381292 GCAGCAAAGCTATTTCCTGACAAT 60.381 41.667 0.00 0.00 36.40 2.71
1665 2161 2.489329 TGCAGCAAAGCTATTTCCTGAC 59.511 45.455 0.00 0.00 36.40 3.51
1671 2192 4.142513 GCTAGAACTGCAGCAAAGCTATTT 60.143 41.667 15.27 0.00 36.40 1.40
1675 2196 1.163554 GCTAGAACTGCAGCAAAGCT 58.836 50.000 15.27 6.63 40.77 3.74
1712 2234 8.408043 ACTGTTGGATTGAACATTAGAATCAA 57.592 30.769 0.00 0.00 35.32 2.57
1746 2440 9.715121 AAATTATGTCTCAAGATTGCAAATTGT 57.285 25.926 20.75 9.17 0.00 2.71
1772 2466 7.341445 AGGTTTAGTGTCAATACAGCAAAAA 57.659 32.000 0.00 0.00 35.91 1.94
1774 2468 6.952773 AAGGTTTAGTGTCAATACAGCAAA 57.047 33.333 0.00 0.00 35.91 3.68
1775 2469 6.952773 AAAGGTTTAGTGTCAATACAGCAA 57.047 33.333 0.00 0.00 35.91 3.91
1776 2470 6.428771 GGTAAAGGTTTAGTGTCAATACAGCA 59.571 38.462 0.00 0.00 35.91 4.41
1777 2471 6.653740 AGGTAAAGGTTTAGTGTCAATACAGC 59.346 38.462 0.00 0.00 35.91 4.40
1778 2472 8.617290 AAGGTAAAGGTTTAGTGTCAATACAG 57.383 34.615 0.00 0.00 35.91 2.74
1779 2473 7.662669 GGAAGGTAAAGGTTTAGTGTCAATACA 59.337 37.037 0.00 0.00 0.00 2.29
1780 2474 7.148523 CGGAAGGTAAAGGTTTAGTGTCAATAC 60.149 40.741 0.00 0.00 0.00 1.89
1782 2476 5.704053 CGGAAGGTAAAGGTTTAGTGTCAAT 59.296 40.000 0.00 0.00 0.00 2.57
1783 2477 5.058490 CGGAAGGTAAAGGTTTAGTGTCAA 58.942 41.667 0.00 0.00 0.00 3.18
1784 2478 4.634199 CGGAAGGTAAAGGTTTAGTGTCA 58.366 43.478 0.00 0.00 0.00 3.58
1786 2480 3.181452 TGCGGAAGGTAAAGGTTTAGTGT 60.181 43.478 0.00 0.00 0.00 3.55
1787 2481 3.404899 TGCGGAAGGTAAAGGTTTAGTG 58.595 45.455 0.00 0.00 0.00 2.74
1856 4270 6.541278 TGCAATGCTCATATAGATATCTTGCC 59.459 38.462 11.25 0.00 0.00 4.52
1941 4360 3.928005 ATCTGTTCATGTGCATCCTCT 57.072 42.857 0.00 0.00 0.00 3.69
1976 4395 1.297456 GCTCTCCTTCAGTGCAGTGC 61.297 60.000 17.07 8.58 40.73 4.40
2046 4465 0.394352 CAGGATGGCGGCTAAAGGTT 60.394 55.000 11.43 0.00 0.00 3.50
2114 4533 7.685155 GCCAACTGCCATCTCATTATTGTTATT 60.685 37.037 0.00 0.00 0.00 1.40
2123 4542 1.822990 CAAGCCAACTGCCATCTCATT 59.177 47.619 0.00 0.00 42.71 2.57
2150 4621 3.062122 TGAGCAGTTCATCAGCATCAA 57.938 42.857 0.00 0.00 0.00 2.57
2156 4627 3.340928 TGACCAATGAGCAGTTCATCAG 58.659 45.455 0.00 0.00 45.82 2.90
2291 4762 1.219393 GCTCTACGAAGGCCTTGCT 59.781 57.895 26.25 9.90 0.00 3.91
2450 4921 1.555967 GGGCCAGCAAACAAATAGGA 58.444 50.000 4.39 0.00 0.00 2.94
2541 5012 1.676968 CCAATCACCACTCGGTCCA 59.323 57.895 0.00 0.00 44.71 4.02
2585 5056 3.349927 CATGCAGGAAGTCCTTCATCAA 58.650 45.455 9.25 0.00 44.79 2.57
2608 5079 3.273080 CTTCAGCCGGGTTGCAAGC 62.273 63.158 20.26 20.26 0.00 4.01
3043 5591 4.156477 TCGGTGACACATCATGGGATATA 58.844 43.478 8.08 0.00 37.14 0.86
3047 5595 1.203237 ATCGGTGACACATCATGGGA 58.797 50.000 8.08 0.00 37.14 4.37
3075 5654 9.559732 CTTACATCAAACCACCTGATAATATGA 57.440 33.333 0.00 0.00 32.20 2.15
3087 5666 6.861065 TTTGAGACTCTTACATCAAACCAC 57.139 37.500 3.68 0.00 36.89 4.16
3154 5744 3.370978 ACTGACACAAACAAGTCTTGTCG 59.629 43.478 18.42 14.53 44.59 4.35
3161 5751 6.229936 TCCTACTTACTGACACAAACAAGT 57.770 37.500 0.00 0.00 0.00 3.16
3312 5902 4.409570 CAATGAAGGAAATGACTCGCTTG 58.590 43.478 0.00 0.00 0.00 4.01
3400 5993 8.764287 GCCGCATATTTTGATAAGCTTTAAATT 58.236 29.630 3.20 4.11 0.00 1.82
3717 9657 2.669240 GAGTCTTTCCCCCGGGTG 59.331 66.667 21.85 8.67 36.47 4.61
3725 9665 1.064825 TTCAGGTGGGGAGTCTTTCC 58.935 55.000 0.00 0.00 46.00 3.13
3764 9704 6.956299 AATTTCATTGCAATGCAGTACTTC 57.044 33.333 30.57 0.00 40.61 3.01
3796 9736 2.557056 CTCTGTTCGGACCTACAGACAA 59.443 50.000 17.63 3.85 44.20 3.18
3982 9924 3.190383 TGAGGATCTTTGGAGACCTGA 57.810 47.619 0.00 0.00 35.16 3.86
4053 9996 8.472413 AGTGGACTCAAATGGATCATTTATTTG 58.528 33.333 13.38 13.38 41.40 2.32
4062 10005 2.019984 GGCAGTGGACTCAAATGGATC 58.980 52.381 0.00 0.00 0.00 3.36
4082 10025 3.726517 CCGTGAGCCCTTGCAACG 61.727 66.667 0.00 0.00 44.57 4.10
4097 10040 5.298527 TGAGACCATCTATGTACAGTAACCG 59.701 44.000 0.33 0.00 0.00 4.44
4235 15491 8.586273 CACTAATGTTTTTGAGAAACACAACAG 58.414 33.333 3.26 2.26 42.18 3.16
4253 15509 6.142817 GCAATTTGTTTCGTCTCACTAATGT 58.857 36.000 0.00 0.00 0.00 2.71
4261 15517 4.593095 GAAACGCAATTTGTTTCGTCTC 57.407 40.909 14.12 0.00 43.83 3.36
4273 15529 3.932710 TCTTCGCATTCTAGAAACGCAAT 59.067 39.130 22.78 0.48 0.00 3.56
4318 15574 8.484641 TTGCAATTTGTTTTGACATTCAGTAA 57.515 26.923 0.00 0.00 0.00 2.24
4319 15575 8.549548 CATTGCAATTTGTTTTGACATTCAGTA 58.450 29.630 9.83 0.00 0.00 2.74
4320 15576 6.981762 TTGCAATTTGTTTTGACATTCAGT 57.018 29.167 0.00 0.00 0.00 3.41
4321 15577 7.631822 TCATTGCAATTTGTTTTGACATTCAG 58.368 30.769 9.83 0.00 0.00 3.02
4322 15578 7.549615 TCATTGCAATTTGTTTTGACATTCA 57.450 28.000 9.83 0.00 0.00 2.57
4323 15579 8.838452 TTTCATTGCAATTTGTTTTGACATTC 57.162 26.923 9.83 0.00 0.00 2.67
4324 15580 9.074443 GTTTTCATTGCAATTTGTTTTGACATT 57.926 25.926 9.83 0.00 0.00 2.71
4325 15581 8.460428 AGTTTTCATTGCAATTTGTTTTGACAT 58.540 25.926 9.83 0.00 0.00 3.06
4326 15582 7.814642 AGTTTTCATTGCAATTTGTTTTGACA 58.185 26.923 9.83 0.00 0.00 3.58
4327 15583 7.961827 TGAGTTTTCATTGCAATTTGTTTTGAC 59.038 29.630 9.83 1.37 0.00 3.18
4328 15584 8.037382 TGAGTTTTCATTGCAATTTGTTTTGA 57.963 26.923 9.83 0.25 0.00 2.69
4329 15585 8.670804 TTGAGTTTTCATTGCAATTTGTTTTG 57.329 26.923 9.83 0.00 32.27 2.44
4330 15586 9.291664 CATTGAGTTTTCATTGCAATTTGTTTT 57.708 25.926 9.83 0.00 32.27 2.43
4331 15587 8.675504 TCATTGAGTTTTCATTGCAATTTGTTT 58.324 25.926 9.83 0.00 35.60 2.83
4332 15588 8.211116 TCATTGAGTTTTCATTGCAATTTGTT 57.789 26.923 9.83 0.00 35.60 2.83
4333 15589 7.789273 TCATTGAGTTTTCATTGCAATTTGT 57.211 28.000 9.83 0.00 35.60 2.83
4334 15590 7.270365 GCATCATTGAGTTTTCATTGCAATTTG 59.730 33.333 9.83 0.68 35.60 2.32
4335 15591 7.041030 TGCATCATTGAGTTTTCATTGCAATTT 60.041 29.630 9.83 0.00 34.89 1.82
4336 15592 6.428465 TGCATCATTGAGTTTTCATTGCAATT 59.572 30.769 9.83 0.00 34.89 2.32
4337 15593 5.935206 TGCATCATTGAGTTTTCATTGCAAT 59.065 32.000 5.99 5.99 34.89 3.56
4338 15594 5.177881 GTGCATCATTGAGTTTTCATTGCAA 59.822 36.000 0.00 0.00 37.22 4.08
4339 15595 4.687018 GTGCATCATTGAGTTTTCATTGCA 59.313 37.500 3.79 3.79 35.60 4.08
4340 15596 4.927425 AGTGCATCATTGAGTTTTCATTGC 59.073 37.500 0.00 0.00 35.60 3.56
4341 15597 5.575606 GGAGTGCATCATTGAGTTTTCATTG 59.424 40.000 0.00 0.00 36.49 2.82
4342 15598 5.337009 GGGAGTGCATCATTGAGTTTTCATT 60.337 40.000 0.00 0.00 32.27 2.57
4343 15599 4.159135 GGGAGTGCATCATTGAGTTTTCAT 59.841 41.667 0.00 0.00 32.27 2.57
4344 15600 3.507233 GGGAGTGCATCATTGAGTTTTCA 59.493 43.478 0.00 0.00 0.00 2.69
4345 15601 3.507233 TGGGAGTGCATCATTGAGTTTTC 59.493 43.478 0.00 0.00 0.00 2.29
4346 15602 3.499338 TGGGAGTGCATCATTGAGTTTT 58.501 40.909 0.00 0.00 0.00 2.43
4347 15603 3.087031 CTGGGAGTGCATCATTGAGTTT 58.913 45.455 0.00 0.00 0.00 2.66
4357 15614 1.133513 TGTTTTCACCTGGGAGTGCAT 60.134 47.619 0.00 0.00 37.68 3.96
4366 15623 6.979817 TGACATTCAGAAATTGTTTTCACCTG 59.020 34.615 1.74 0.00 43.09 4.00
4367 15624 7.111247 TGACATTCAGAAATTGTTTTCACCT 57.889 32.000 1.74 0.00 43.09 4.00
4489 15751 6.560253 TCATAAGAAAAGAGCACTGAAACC 57.440 37.500 0.00 0.00 0.00 3.27
4568 16192 3.576982 AGATGTGAAACGGACAGGACTAA 59.423 43.478 0.00 0.00 42.39 2.24
4569 16193 3.162666 AGATGTGAAACGGACAGGACTA 58.837 45.455 0.00 0.00 42.39 2.59
4576 16200 3.870633 AGGTAGAGATGTGAAACGGAC 57.129 47.619 0.00 0.00 42.39 4.79
4578 16202 9.976511 TTAATATTAGGTAGAGATGTGAAACGG 57.023 33.333 0.00 0.00 42.39 4.44
4657 16286 5.703130 CAGACAGCTCCCTTTAATATTAGGC 59.297 44.000 0.00 0.00 0.00 3.93
4683 16312 5.991328 AAATATCATGGTCATGTGTCGAC 57.009 39.130 9.11 9.11 39.72 4.20
4918 16549 2.290832 TGCTGTCCAATTGATGCTGGTA 60.291 45.455 7.12 0.00 34.11 3.25
4948 16579 1.801178 GCCAGAAACGACCTTGAAGAG 59.199 52.381 0.00 0.00 0.00 2.85
4949 16580 1.872237 CGCCAGAAACGACCTTGAAGA 60.872 52.381 0.00 0.00 0.00 2.87
4950 16581 0.512952 CGCCAGAAACGACCTTGAAG 59.487 55.000 0.00 0.00 0.00 3.02
4951 16582 1.503818 GCGCCAGAAACGACCTTGAA 61.504 55.000 0.00 0.00 0.00 2.69
4952 16583 1.959226 GCGCCAGAAACGACCTTGA 60.959 57.895 0.00 0.00 0.00 3.02
4953 16584 2.250939 TGCGCCAGAAACGACCTTG 61.251 57.895 4.18 0.00 0.00 3.61
4954 16585 2.110213 TGCGCCAGAAACGACCTT 59.890 55.556 4.18 0.00 0.00 3.50
4955 16586 2.665185 GTGCGCCAGAAACGACCT 60.665 61.111 4.18 0.00 0.00 3.85
4956 16587 3.723348 GGTGCGCCAGAAACGACC 61.723 66.667 12.58 0.00 34.09 4.79
4957 16588 4.072088 CGGTGCGCCAGAAACGAC 62.072 66.667 18.18 0.00 34.09 4.34
4958 16589 4.287781 TCGGTGCGCCAGAAACGA 62.288 61.111 18.18 2.37 34.09 3.85
4959 16590 4.072088 GTCGGTGCGCCAGAAACG 62.072 66.667 18.18 0.00 34.09 3.60


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.